Yes I would like to open with fslview (FSL) the sig.nii.gz of each
subject which is computed by seed-based analysis by FS-FAST.
I have mask the sig.nii.gz by fslmaths -div
I have run:
mri_vol2surf --src sig_mask.nii.gz --src_type nii.gz --srcreg
subj/rest/001/register.dof6.dat --hemi rh --o prova
Hi Stefano
mri_vol2surf samples the volume onto the surface and saves it as a 1D
list of values, one per surface vertex. You can't view that in fslview
AFAIK - you need to load a surface in freeview/tksurfer and visualize it
as an overlay on the surface.
cheers
Bruce
On Tue, 27 Oct 2015, std..
Dear Freesurfers,
I am trying to use 3dclustsim in AFNI to determine the minimum number of
voxel in a cluster to reach significance, my understanding is that in the
command line the -fwhm s flag refers to the gaussian filter width and NOT
the Gaussian Kernel, can anyone point me to how I might be a
yes, use mri_glmfit
doug
On 10/26/15 3:34 AM, Sandy Schramm wrote:
> Dear Experts,
>
> we want to compare data (thickness) of 4 groups (3 morbid groups and 1
> controll group). Both, Qdec and mri_glmfit, will do the same analyses.
> But we are not sure, if the usage of Qdec is statistically correc
It may cover both, but the peak can only be in one, and it is the peak
that is reported.
On 10/25/15 9:55 AM, Annemarie Brandhofe wrote:
Dear freesurfer experts,
I have analyzed inter-group differences in cortical thickness using
freesurfer 5.3.0 and QDEC. I have found one significiant clu
The indices should be different. Eg, 17 is left hippo, 53 is right
hippo. If you click on them in freeview and different labels appear,
then FS knows they are different
On 10/24/15 9:29 PM, Jacobs H (NP) wrote:
> Hi.
>
> Just one another related question: now that I was able to combine left and
>
We changed the name to "unsegmented white matter" because we don't know
whether they really represent centrum semiovale. We don't have an ROI
that has been verified to be CS.
doug
On 10/25/15 7:10 PM, Syeda Maryam wrote:
Hello Freesurfer experts,
I needed to extract the centrum semiovale fro
I think the problem is probably that you created the label from a volume
whereas funcroi expects the label to come from a surface. Instead of
using mri_cor2label and -label for funcroi-config, try using something like
funcroi-config -annot aparc.a2009s G_and_S_cingul-Ant -analysis
analysis_i
Hello,
I used recon-all -hippo subfields on an earlier version of free surfer
(recon v 5.0, hippo v5.0 or 5.1). There is no documentation on your website
on how to view the subfields in freeview with versions earlier than 5.2. I
noticed when I load all the subfields into free view and use the colo
Hi Doug,
Yes, for the aseg they are. But not for the hippocampal subfields: left
and right have the same color coding.
I am creating one segmentation, including left and right hippocampal
subfields and aparc, for partial volume correction.
Any idea how I can make the labels for the hippocampal sub
The color is not important. The question is whether they have a
different index. Can you confirm that lh and rh have the same index?
On 10/27/15 11:53 AM, Jacobs H (NP) wrote:
> Hi Doug,
>
> Yes, for the aseg they are. But not for the hippocampal subfields: left
> and right have the same color cod
Hi Danielle,
from the mri directory of a subject, run
freeview nu.mgz -p-labels posterior_left_* posterior_Left-Hippocampus.mgz
-p-labels posterior_right_* posterior_Right-Hippocampus.mgz -p-prefix
posterior_ -p-lut $FREESURFER_HOME/FreeSurferColorLUT.txt
and be a bit patient; it takes a li
I just checked again in freeview and indeed they have the same index (e.g.
CA1 has value 206 for left and also for right).
On 10/27/15, 5:01 PM, "Douglas Greve" wrote:
>The color is not important. The question is whether they have a
>different index. Can you confirm that lh and rh have the same
Hi Doug,
Thanks for the help! So, you’re saying that:
By specifying a volume file (ie: aparc.a2009s+aseg.mgz) when using
mri_cor2label, I’ve created volume labels
The commands ‘funcroi-config' and 'funcroi-table-sess' accept only labels
created on the surface.
Is this correct?
Thanks,
Keji
On 10/27/15 1:09 PM, Morenikeji Adebayo wrote:
Hi Doug,
Thanks for the help! So, you’re saying that:
1. By specifying a volume file (ie: aparc.a2009s+aseg.mgz) when
using mri_cor2label, I’ve created volume labels
Correct
1. The commands ‘funcroi-config' and 'funcroi-table-sess' ac
Thank you for your input. I noticed that if I follow literally all the steps in
the wiki, my data which is ordered by variable 'family' (instead of subjects,
in my case is number of members belonging to e.g. family_1) is shuffled. This
happens after I run the command sortData below. Especiall
Hi Freesurfers,
I am interested in running a functional connectivity analysis outside of the
Freesurfer environment, using freesurfer-derived ROIs
I've run recon-all, and I have run preproc-sess to carry out initial fmri
preprocessing steps (motion correction, warping to the anatomical, etc)
Hi everybody. Could anyone help me please?
I've downloaded FreeSurfer source code to compile and install on Ubuntu
12.04, but I've got an error when try to run the *configure* file.
The log is below:
root@ubuntu:~/freesurfer-source/freesurfer# ./configure
--prefix=/root/freesurfer-inst --enable
Hi everybody. Could anyone help me please?
I've downloaded minc-tools source code to compile and install on Ubuntu
12.04, but I've got an error when try to run the *configure* file.
The log is below:
root@ubuntu:~/freesurfer-source/minc-tools/minc-2.1.00# ./configure
--prefix=/root/freesurfer-i
Hi,
I'm running into an issue where the slices from one DICOM series are being
parsed by mri_parse_sdcmdir (and mri_info and mri_convert) as two separate
series.
A few example lines from a scan.out:
6 AR_t.s40.c0 ok 64 64 41 1
7 AR_t.s40.c0 ok 64 64 23 1
Th
Postdoc Positions for the Adolescent Brain Cognitive Development (ABCD) study
University of California, San Diego
Several funded postdoctoral positions are available in image analysis method
development, including automated cortical- and subcortical segmentation,
advanced diffusion tracto
Dear Bruce,
Am I missed the answer of Dr. Greve about the following questions?
Is it possible to tell what are the implemented methods for the PET pve
correction? and how we can
obtain the corrected 4D (dynamic) PET images (for a voxel-by-voxel modeling)?
Many thanks,
Mohamed
On 26/10/15 1
Hi Pablo,
the sortData function sorts the rows so that entries from the same
subject (in your case same family) are blocked and that within each
block the time variable (2nd parameter specifies which column that is in
your M matrix, in your case the first =1) is increasing.
It is important, wh
Hi Mohamed, sorry, I have not fully documented the procedure yet. I've
put some notes below
doug
1. To start, run
gtmseg --s subject
This will take a couple of hours and produces some files needed for GTM
PVC (which is used for GTM, MG, RBV).
2. You'd then register the PET to the anatomical
Hello,
Is the AtlasMesh under the following pathway a standard mesh structure? If
so, what is it? Better yet, is there a way for those meshes in the
AtlasMesh to be converted to a standard stl file or some other standard
mesh file format? To be clear, I know the .gz is a compressed file; I'm
refe
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